Module: Bioroebe::Taxonomy::Shared
Overview
Bioroebe::Taxonomy::Shared
Constant Summary
Constants included
from Constants
Constants::AA_DIR, Constants::ARRAY_PROJECT_FILES, Constants::Archaea_Taxonomy_ID, Constants::BASE, Constants::BASE_URL, Constants::BE_VERBOSE, Constants::Bacteria_Taxonomy_ID, Constants::CITATIONS, Constants::CURATED_DIR, Constants::DATA_DIR, Constants::DELNODES, Constants::DIVISION, Constants::Eukaryota_Taxonomy_ID, Constants::FILE_USE_THIS_DATABASE, Constants::GEM_DIR, Constants::GENCODE, Constants::INCOMING_DIR, Constants::INFO_DIR, Constants::LAST_INTERACTIVE_COMMAND, Constants::LOCALOME_DIR, Constants::LOCAL_MIRROR, Constants::MERGED, Constants::MODULE_PATH, Constants::NAMES, Constants::NAMES_SQL, Constants::NCBI_BASE, Constants::NODES, Constants::NODES_SQL, Constants::NT_DIR, Constants::POSTGRESQL_QUERY_SIZE, Constants::POSTGRE_LOGIN_COMMAND, Constants::PROJECT_DOC_DIR, Constants::SEQUENCES_DIR, Constants::SHARED_HOME, Constants::TAXONOMY_BROWSER, Constants::TEMP_DIR, Constants::TEST_DIR, Constants::TMP_DIR, Constants::URL1
Class Method Summary
collapse
Instance Method Summary
collapse
Methods included from Constants
#info_dir?, #work_directory?
Class Method Details
.be_quiet ⇒ Object
#
Taxonomy::Shared.be_quiet
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 155
def self.be_quiet
@be_verbose = false
end
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.be_verbose? ⇒ Boolean
#
Taxonomy::Shared.be_verbose?
Whether we will be verbose or whether we will be silent.
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 148
def self.be_verbose?
@be_verbose
end
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Instance Method Details
#cd(i = File.expand_path('~'), be_verbose = false) ⇒ Object
#
cd (cd tag, change dir tag)
This method allows for some special shortcuts, such as aa.
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 200
def cd(
i = File.expand_path('~'),
be_verbose = false
)
be_verbose = true if be_verbose == :be_verbose
i = File.expand_path('~') if i.nil?
i = i.to_s
case i when '?',
/^-?-?HELP$/i
e 'You can cd to these special dirs:'
e
e ' '+TEMP_DIR
e ' '+INFO_DIR
e ' '+NT_DIR
e ' '+LOCALOME_DIR
e
return
when /^HOME$/i
i = TEMP_DIR
when 'robert',
'1',
'tmp'
i = TEMP_DIR
when 'aa',
'fasta'
i = AA_DIR
when 'info','i'
i = INFO_DIR
when 'nt',
'dna',
'rna'
i = NT_DIR
when 'local',
'localome',
/^local/,'loc'
i = LOCALOME_DIR
end unless File.exist?(i)
if Dir.exist? i
if be_verbose
e "We will now change directory to #{sdir(i)}."
end
Dir.chdir(i)
else
e "We can not change directory into #{sdir(i)}#{rev} "\
"as this directory does not exist."
end
end
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#edit_login_file(optional_number = '') ⇒ Object
#
edit_login_file
For this we deliberately use the vim editor.
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 171
def edit_login_file(
optional_number = ''
)
esystem "vim #{return_login_file}#{optional_number.to_s}"
end
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#eliminate_tabulator(i) ⇒ Object
Also known as:
sanitize_content
#
eliminate_tabulator
As of now, this method will remove âtâ input and â|â.
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 78
def eliminate_tabulator(i)
i.gsub(/#{TABULATOR}\|/, '')
end
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#ensure_that_download_dir_exists(i = ::Bioroebe.taxonomy_download_directory?) ⇒ Object
#
ensure_that_download_dir_exists
#
#ensure_that_temp_dir_exists ⇒ Object
#
ensure_that_temp_dir_exists
#
#mkdir(i) ⇒ Object
#
mkdir (mkdir tag)
Simple wrapper over creating a directory. We use the Array format.
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 191
def mkdir(i)
::Bioroebe.mkdir(i)
end
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#readlines(i = :names) ⇒ Object
#
readlines
The readlines-wrapper uses File.foreach to iterate over the content.
Typically we can find these files at:
/root/taxonomy/names.dmp
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 101
def readlines(
i = :names
)
i = i.to_sym case i
when :nodes
if File.exist? NODES
return File.foreach(NODES)
else
e 'Warning - the file at '+sfile(NODES)+' does not exist.'
return []
end
when :names
if File.exist? NAMES
return File.foreach(NAMES)
else
e 'Warning - the file at '+sfile(NODES)+' does not exist.'
return []
end
else
i = i.to_s
if File.exist? i
return File.foreach(i)
else
e 'Do not know what to do with input: '+sfancy(i)
end
end
end
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#set_pgpassword ⇒ Object
Also known as:
set_password
#
set_pgpassword (password tag)
Set the password for Postgresql here.
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 275
def set_pgpassword
::Bioroebe.set_pgpassword
end
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#show_password ⇒ Object
#
show_password
This shows the password.
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 50
def show_password
e 'The current password for the Postgresql login is:'
e
e " #{sfancy(POSTGRE_PASSWORD)}"
e
end
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#show_time_now ⇒ Object
Also known as:
show_current_time
#
show_time_now
This will show the current time.
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 182
def show_time_now
::Bioroebe.show_time_now
end
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#split_at(i) ⇒ Object
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# File 'lib/bioroebe/taxonomy/shared.rb', line 85
def split_at(i)
return i.split(MAIN_DELIMITER).map(&:chomp).map() {|entry|
eliminate_tabulator(entry)
}
end
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#split_at_tabulator(i) ⇒ Object
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# File 'lib/bioroebe/taxonomy/shared.rb', line 69
def split_at_tabulator(i)
i.split(FIELD_TERMINATOR) if i.is_a? String
end
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#tokenize(i) ⇒ Object
#
tokenize
We will split at the given input. Input is expected to be a string.
#
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# File 'lib/bioroebe/taxonomy/shared.rb', line 62
def tokenize(i)
i.split(TOKEN).map(&:strip)
end
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